Mercurial > repos > iuc > bcftools_convert_to_vcf

comparison test-data/annotate.vcf @ 0:b068ef999550 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:02:49 -0400
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-1:000000000000 0:b068ef999550
1 ##fileformat=VCFv4.1
2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
3 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
9 ##FILTER=<ID=q10,Description="Quality below 10">
10 ##FILTER=<ID=test,Description="Testing filter">
11 ##contig=<ID=1,assembly=b37,length=249250621>
12 ##contig=<ID=2,assembly=b37,length=249250621>
13 ##contig=<ID=3,assembly=b37,length=198022430>
14 ##contig=<ID=4,assembly=b37,length=191154276>
15 ##test=<ID=4,IE=5>
16 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
17 ##readme=AAAAAA
18 ##readme=BBBBBB
19 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
20 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
21 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
22 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
24 1 3000150 . C T 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
25 1 3000151 . C T 59.2 PASS AN=4;AC=2 GT:DP:GQ 0/1:32:245 0/1:32:245
26 1 3062915 id3D GTTT G 12.9 q10 DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20
27 1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4;AN=3;AC=1,1 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 2:0,1:409:35:-20,-5,-20
28 1 3106154 . CAAA C 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
29 1 3106154 . C CT 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
30 1 3157410 . GA G 90.6 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:21:21
31 1 3162006 . GAA G 60.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:212:22 0/1:212:22
32 1 3177144 . G T 45 PASS AN=4;AC=2 GT:GQ:DP 0/0:150:30 1/1:150:30
33 1 3177144 . G . 45 PASS AN=4;AC=0 GT:GQ:DP 0/0:150:30 0/0:150:30
34 1 3184885 . TAAAA TA,T 61.5 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:12:10 1/2:12:10
35 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26
36 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26
37 4 3258448 . TACACACAC T 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
38 4 4000000 . T A,C 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
39 4 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31